I want to apply the adjustment layer to the raster layers below it, "rasterizing" it basically, so that the pixels in layers 3 & 4 are changed based on the adjustment layer. I don't want to modify the layer stack in any way. That is, no creating or removing layers. Layer 3 and 4 must stay exactly as they are, just the pixels in them should be changed. I don't want to do this one layer at a time, is this possible in Photoshop CS4?

Clip the adjustment layer to layer 3 and then clip layer 3 to layer 4 by holding Alt and clicking in between the layers on the line. (The adjustment layer will only affect those layers so you can put some below it)

3.

Select Layers 3 & 4 -> Right Click on one -> Convert to Smart Object -> Apply a filter to that Smart Layer.... You can double click on the smart object to get access to the two layers untouched and edit them directly if needed for whatever reason. If you do edit them directly you need to save the document that is opened by double clicking to alter it in the main document.

Notes:
If you rasterize the adjustment layer into layer 3 and 4 and keep the adjustment layer it will be applied again.

If you use filters you might want to convert layer 3 and 4 to smart objects so you can change/remove the filter.

Personally I would stick with what you have... and maybe clip the adjustment layer because it is non-destructive applying them directly unnecessarily destroys information.

Adjustment layers aren't actually changing the pixel data of the layers below it is only an overlay. Photoshop is very weak when it comes to doing permanent changes to multiple layers of data and it makes it really hard for animations and layers that all need to be globally changed at the data level.

I'm also trying to find out how to rasterize/merge the layer adjustments to the layer data itself and so far not much luck other than exporting layers with batch operations.